In a previous genome-wide linkage scan for genes predisposing to type 2 diabetes mellitus (T2DM) in the Pima Indians, we obtained the strongest evidence for linkage with markers on chromosome 1q21-q23. Subsequently, the 1q linkage of T2DM has been replicated in several, diverse populations. Our strategy to search for the underlying diabetes susceptibility gene(s) has been based on two complementary approaches: 1) systematic analysis of densely spaced single nucleotide polymorphisms (SNPs); and 2) investigation of candidate genes within the linked region for variants/mutations. Informative SNPs are tested for association with diabetes, and their effect on the linkage is also evaluated. For the systematic analysis of single nucleotide polymorphisms, an international collaborative Chromosome 1 Consortium has been established by uniting several of the groups which detected T2DM linkage on 1q, with the goal to facilitate search for the underlying diabetes gene(s). This startegy involves analysis of over 5000 subjects from five populations (including about 1000 Pimas), and so far this effort has led to genotyping of over 4900 SNPs within an initial interval of 21 Mb spanning the linkage peak in most populations. To date, more than 150 candidate genes have been analyzed by sequencing in a subset of diabetic and non-diabetic Pimas. In addition, our lab at NIDDK has investiagted more than 150 candidiate genes. CACNA1E was sequenced as a positional candidate gene for this linkage and 30 SNPs were genotyped in the same group of Pima Indians who had been analyzed in the linkage study. A novel G/A variant located in the 3UTR was associated with young-onset T2DM (odds ratio=2.09 per copy of the G allele; 95% CI=1.31-3.33, adjusted p=0.001 and p=0.0006 under an additive and recessive model, respectively) and had a significant effect upon the evidence for linkage at chromosome 1q21-25 (p=0.004). In addition, among 372 non-diabetic Pima subjects who had undergone metabolic testing, this variant was associated with multiple measures of reduced insulin action that included increased fasting, 30, 60 and 120 minute plasma glucose concentrations and increased fasting plasma insulin during an oral glucose tolerance test (all adjusted p<0.01) as well as a decreased rate of insulin-stimulated glucose disposal at both physiologically and maximally stimulated insulin concentrations (both p<0.002). Functional analysis of this 3UTR variant showed that the non-risk allele had a 2.3 fold higher expression as compared to the risk allele. Our data suggest that this 3UTR variant in CACNA1E contributes to T2DM susceptibility among the Pima Indians by effecting whole-body insulin action. In addition, ARHGEF11, which encodes the Rho guanine nucleotide exchange factor 11, was analyzed as a positional candidate gene for this linkage because this protein may stimulate Rho-dependent signals, such as the insulin signaling cascade. The ARHGEF11 gene, and two adjacent genes NTRK1 and INSRR, were sequenced in 24 Pima Indians who were not first-degree relatives. Sequencing of the coding regions, 5and 3 UTRs and putative promoter regions of these genes, identified 28 variants in ARHGEF11, 11 variants in NTRK1 and 8 variants in INSSR. These 47 variants, as well as 84 additional public database variants within/between these genes, were genotyped for association analysis in the same group of Pima Indians who had participated in the linkage study. An R1467H in ARHGEF11, and several additional non-coding variants that were in high linkage disequilibrium with this variant, were nominally associated with young-onset T2DM (P=0.01, OR=3.39) after adjusting for sex, family membership and Pima heritage. The risk allele H had a frequency of 0.10. In a subgroup of 262 on-diabetic full-heritage Pima Indians who had undergone detailed metabolic testing, the risk allele H was also associated with a lower mean insulin-mediated glucose disposal rate and a lower mean non-oxidative glucose storage rate after adjusting for age, sex, nuclear family membership, and percentage of body fat (P0.01). These findings suggest that variation within ARHGEF11 nominally increases risk of T2DM, possibly as a result of increased insulin resistance.